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Computing Maximum-Scoring Segments in Almost Linear Time

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Computing and Combinatorics (COCOON 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4112))

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Abstract

Given a sequence, the problem studied in this paper is to find a set of k disjoint continuous subsequences such that the total sum of all elements in the set is maximized. This problem arises naturally in the analysis of DNA sequences. The previous best known algorithm requires Θ(n log n) time in the worst case. For a given sequence of length n, we present an almost linear-time algorithm for this problem. Our algorithm uses a disjoint-set data structure and requires O(nα(n, n)) time in the worst case, where α(n, n) is the inverse Ackermann function.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Electrical Engineering, Luleå University of Technology, S-970 87, Luleå, Sweden

    Fredrik Bengtsson & jingsen Chen

Authors
  1. Fredrik Bengtsson
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  2. jingsen Chen
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, University of Notre Dame, IN 46556, Notre Dame, USA

    Danny Z. Chen

  2. Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan

    D. T. Lee

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© 2006 Springer-Verlag Berlin Heidelberg

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Bengtsson, F., Chen, j. (2006). Computing Maximum-Scoring Segments in Almost Linear Time. In: Chen, D.Z., Lee, D.T. (eds) Computing and Combinatorics. COCOON 2006. Lecture Notes in Computer Science, vol 4112. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11809678_28

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  • DOI: https://doi.org/10.1007/11809678_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-36925-7

  • Online ISBN: 978-3-540-36926-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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